Untitled

Cue only ! dummy coding

Pain cue

Pain :: load dataset

mount_dir = '/Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel';
con_list = dir(fullfile(mount_dir, '*/con_0018.nii'));
spm('Defaults','fMRI') 
con_fldr = {con_list.folder}; fname = {con_list.name};
con_files = strcat(con_fldr,'/', fname)';
con_data_obj = fmri_data(con_files);
Using default mask: /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/brainmask_canlab.nii
Direct calls to spm_defauts are deprecated.
Please use spm('Defaults',modality) or spm_get_defaults instead.
sampleto = '/Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0018.nii'
loading mask. mapping volumes. 
checking that dimensions and voxel sizes of volumes are the same. 
Pre-allocating data array. Needed: 24360228 bytes
Loading image number:    61
Elapsed time is 151.664213 seconds.
Image names entered, but fullpath attribute is empty. Getting path info.
Number of unique values in dataset: 5934270  Bit rate: 22.50 bits
contrast_name = {'cue_P', 'cue_V', 'cue_C', 'cue_G',...
    'cueXcue_P', 'cueXcue_V', 'cueXcue_C', 'cueXcue_G',...
    'stim_P', 'stim_V', 'stim_C', 'stim_G',...
    'stimXcue_P', 'stimXcue_V', 'stimXcue_C', 'stimXcue_G',...
    'motor', ...
    'simple_cue_P', 'simple_cue_V', 'simple_cue_C',...
    'simple_cueXcue_P', 'simple_cueXcue_V', 'simple_cueXcue_C', ...
    'simple_stim_P', 'simple_stim_V', 'simple_stim_C',...
    'simple_stimXcue_P', 'simple_stimXcue_V', 'simple_stimXcue_C'};

Pain :: check data coverage

m = mean(con_data_obj);
m.dat = sum(~isnan(con_data_obj.dat) & con_data_obj.dat ~= 0, 2);
orthviews(m, 'trans') % display
SPM12: spm_check_registration (v7759)              06:44:19 - 26/05/2022
========================================================================
Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1
Grouping contiguous voxels:   1 regions
ans = 1×1 cell array
    {1×1 region}

Pain :: Plot diagnostics, before l2norm

drawnow; snapnow

[wh_outlier_uncorr, wh_outlier_corr] = plot(con_data_obj)

______________________________________________________________ Outlier analysis ______________________________________________________________ global mean | global mean to var | spatial MAD | Missing values | 0 images Retained 10 components for mahalanobis distance Expected 50% of points within 50% normal ellipsoid, found 24.59% Expected 3.05 outside 95% ellipsoid, found 11 Potential outliers based on mahalanobis distance: Bonferroni corrected: 8 images Cases 5 10 14 28 31 37 40 57 Uncorrected: 11 images Cases 5 10 14 21 28 31 37 40 44 55 57 Retained 15 components for mahalanobis distance Expected 50% of points within 50% normal ellipsoid, found 54.10% Expected 3.05 outside 95% ellipsoid, found 4 Potential outliers based on mahalanobis distance: Bonferroni corrected: 0 images Cases Uncorrected: 4 images Cases 1 14 28 54 Mahalanobis (cov and corr, q<0.05 corrected): 8 images Outlier_count Percentage _____________ __________ global_mean 1 1.6393 global_mean_to_variance 6 9.8361 missing_values 0 0 rmssd_dvars 0 0 spatial_variability 0 0 mahal_cov_uncor 11 18.033 mahal_cov_corrected 8 13.115 mahal_corr_uncor 4 6.5574 mahal_corr_corrected 0 0 Overall_uncorrected 13 21.311 Overall_corrected 8 13.115

SPM12: spm_check_registration (v7759) 06:44:57 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1 (all) /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1 /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

Grouping contiguous voxels: 1 regions

wh_outlier_uncorr = 61×1 logical array

wh_outlier_corr = 61×1 logical array

Pain :: run robfit

set(gcf,'Visible','on')

figure ('Visible', 'on');

drawnow, snapnow;

Pain :: remove outliers based on plot

con = con_data_obj;
disp(strcat("current length is ", num2str(size(con_data_obj.dat,2))))
current length is 61
%for s = 1:length(wh_outlier_corr)
    %disp(strcat("-------subject", num2str(s), "------"))
con.dat = con_data_obj.dat(:,~wh_outlier_corr);
con.image_names = con_data_obj.image_names(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×53 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [53×12 char]
              fullpath: [61×109 char]
           files_exist: [61×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0018.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
con.fullpath = con_data_obj.fullpath(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×53 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [53×12 char]
              fullpath: [53×109 char]
           files_exist: [61×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0018.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
con.files_exist = con_data_obj.files_exist(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×53 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [53×12 char]
              fullpath: [53×109 char]
           files_exist: [53×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0018.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
%end
disp(strcat("after removing ", num2str(sum(wh_outlier_corr)), " participants, size is now ",num2str(size(con.dat,2))))
after removing 8 participants, size is now 53

Pain :: plot diagnostics, after l2norm

imgs2 = con.rescale('l2norm_images');

Pain :: ttest

t = ttest(imgs2);

One-sample t-test Calculating t-statistics and p-values

orthviews(t)

SPM12: spm_check_registration (v7759) 06:45:03 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

ans = 1×1 cell array

{1×1 struct}

drawnow, snapnow;

fdr_t = threshold(t, .05, 'fdr');

Image 1 FDR q < 0.050 threshold is 0.035550 Image 1 10 contig. clusters, sizes 1 to 70885 Positive effect: 70916 voxels, min p-value: 0.00000000 Negative effect: 72 voxels, min p-value: 0.00128245

orthviews(fdr_t)

SPM12: spm_check_registration (v7759) 06:45:05 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

ans = 1×1 cell array

{1×10 struct}

drawnow, snapnow;

create_figure('montage'); axis off

montage(fdr_t)

Setting up fmridisplay objects

sagittal montage: 1274 voxels displayed, 69714 not displayed on these slices

sagittal montage: 1607 voxels displayed, 69381 not displayed on these slices

sagittal montage: 1261 voxels displayed, 69727 not displayed on these slices

axial montage: 13318 voxels displayed, 57670 not displayed on these slices

axial montage: 14118 voxels displayed, 56870 not displayed on these slices

ans =

fmridisplay with properties: overlay: '/Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img' SPACE: [1×1 struct] activation_maps: {[1×1 struct]} montage: {[1×1 struct] [1×1 struct] [1×1 struct] [1×1 struct] [1×1 struct]} surface: {} orthviews: {} history: {} history_descrip: [] additional_info: ''

drawnow, snapnow;

Vicarious cue

clear all

Vicarious :: load dataset

mount_dir = '/Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel';
con_list = dir(fullfile(mount_dir, '*/con_0019.nii'));
spm('Defaults','fMRI') 
con_fldr = {con_list.folder}; fname = {con_list.name};
con_files = strcat(con_fldr,'/', fname)';
con_data_obj = fmri_data(con_files);
Using default mask: /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/brainmask_canlab.nii
Direct calls to spm_defauts are deprecated.
Please use spm('Defaults',modality) or spm_get_defaults instead.
sampleto = '/Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0019.nii'
loading mask. mapping volumes. 
checking that dimensions and voxel sizes of volumes are the same. 
Pre-allocating data array. Needed: 24360228 bytes
Loading image number:    61
Elapsed time is 162.831692 seconds.
Image names entered, but fullpath attribute is empty. Getting path info.
Number of unique values in dataset: 5951534  Bit rate: 22.50 bits
contrast_name = {'cue_P', 'cue_V', 'cue_C', 'cue_G',...
    'cueXcue_P', 'cueXcue_V', 'cueXcue_C', 'cueXcue_G',...
    'stim_P', 'stim_V', 'stim_C', 'stim_G',...
    'stimXcue_P', 'stimXcue_V', 'stimXcue_C', 'stimXcue_G',...
    'motor', ...
    'simple_cue_P', 'simple_cue_V', 'simple_cue_C',...
    'simple_cueXcue_P', 'simple_cueXcue_V', 'simple_cueXcue_C', ...
    'simple_stim_P', 'simple_stim_V', 'simple_stim_C',...
    'simple_stimXcue_P', 'simple_stimXcue_V', 'simple_stimXcue_C'};

Vicarious :: check data coverage

m = mean(con_data_obj);

m.dat = sum(~isnan(con_data_obj.dat) & con_data_obj.dat ~= 0, 2);

orthviews(m, 'trans') % display

SPM12: spm_check_registration (v7759) 06:48:19 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

Grouping contiguous voxels: 1 regions

ans = 1×1 cell array

{1×1 region}

Vicarious :: Plot diagnostics, before l2norm

drawnow; snapnow

[wh_outlier_uncorr, wh_outlier_corr] = plot(con_data_obj)

______________________________________________________________ Outlier analysis ______________________________________________________________ global mean | global mean to var | spatial MAD | Missing values | 0 images Retained 5 components for mahalanobis distance Expected 50% of points within 50% normal ellipsoid, found 18.03% Expected 3.05 outside 95% ellipsoid, found 6 Potential outliers based on mahalanobis distance: Bonferroni corrected: 5 images Cases 10 28 29 50 57 Uncorrected: 6 images Cases 10 19 28 29 50 57 Retained 17 components for mahalanobis distance Expected 50% of points within 50% normal ellipsoid, found 50.82% Expected 3.05 outside 95% ellipsoid, found 0 Potential outliers based on mahalanobis distance: Bonferroni corrected: 0 images Cases Uncorrected: 0 images Cases Mahalanobis (cov and corr, q<0.05 corrected): 5 images Outlier_count Percentage _____________ __________ global_mean 3 4.918 global_mean_to_variance 5 8.1967 missing_values 0 0 rmssd_dvars 0 0 spatial_variability 1 1.6393 mahal_cov_uncor 6 9.8361 mahal_cov_corrected 5 8.1967 mahal_corr_uncor 0 0 mahal_corr_corrected 0 0 Overall_uncorrected 6 9.8361 Overall_corrected 5 8.1967

SPM12: spm_check_registration (v7759) 06:48:57 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1 (all) /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1 /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

Grouping contiguous voxels: 1 regions

wh_outlier_uncorr = 61×1 logical array

wh_outlier_corr = 61×1 logical array

Vicarious :: run robfit

set(gcf,'Visible','on')
figure ('Visible', 'on');
drawnow, snapnow;

Vicarious :: remove outliers based on plot

con = con_data_obj;
disp(strcat("current length is ", num2str(size(con_data_obj.dat,2))))
current length is 61
%for s = 1:length(wh_outlier_corr)
  %  disp(strcat("-------subject", num2str(s), "------"))
con.dat = con_data_obj.dat(:,~wh_outlier_corr);
con.image_names = con_data_obj.image_names(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×56 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [56×12 char]
              fullpath: [61×109 char]
           files_exist: [61×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0019.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
con.fullpath = con_data_obj.fullpath(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×56 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [56×12 char]
              fullpath: [56×109 char]
           files_exist: [61×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0019.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
con.files_exist = con_data_obj.files_exist(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×56 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [56×12 char]
              fullpath: [56×109 char]
           files_exist: [56×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0019.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
%end
disp(strcat("after removing ", num2str(sum(wh_outlier_corr)), " participants, size is now ",num2str(size(con.dat,2))))
after removing 5 participants, size is now 56

Vicarious :: plot diagnostics, after l2norm

imgs2 = con.rescale('l2norm_images');

Vicarious :: ttest

t = ttest(imgs2);

One-sample t-test Calculating t-statistics and p-values

orthviews(t)

SPM12: spm_check_registration (v7759) 06:49:03 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

ans = 1×1 cell array

{1×1 struct}

drawnow, snapnow;

fdr_t = threshold(t, .05, 'fdr');

Image 1 FDR q < 0.050 threshold is 0.016120 Image 1 66 contig. clusters, sizes 1 to 31290 Positive effect: 32077 voxels, min p-value: 0.00000000 Negative effect: 116 voxels, min p-value: 0.00018430

orthviews(fdr_t)

SPM12: spm_check_registration (v7759) 06:49:04 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

ans = 1×1 cell array

{1×66 struct}

drawnow, snapnow;

create_figure('montage'); axis off

montage(fdr_t)

Setting up fmridisplay objects

sagittal montage: 453 voxels displayed, 31740 not displayed on these slices

sagittal montage: 638 voxels displayed, 31555 not displayed on these slices

sagittal montage: 391 voxels displayed, 31802 not displayed on these slices

axial montage: 5805 voxels displayed, 26388 not displayed on these slices

axial montage: 6364 voxels displayed, 25829 not displayed on these slices

ans =

drawnow, snapnow;

Cognitive cue

Cognitive :: load dataset

mount_dir = '/Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel';
con_list = dir(fullfile(mount_dir, '*/con_0020.nii'));
spm('Defaults','fMRI') 
con_fldr = {con_list.folder}; fname = {con_list.name};
con_files = strcat(con_fldr,'/', fname)';
con_data_obj = fmri_data(con_files);
Using default mask: /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/brainmask_canlab.nii
sampleto = '/Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0020.nii'
loading mask. mapping volumes. 
checking that dimensions and voxel sizes of volumes are the same. 
Pre-allocating data array. Needed: 24360228 bytes
Loading image number:    61
Elapsed time is 162.035662 seconds.
Image names entered, but fullpath attribute is empty. Getting path info.
Number of unique values in dataset: 5940111  Bit rate: 22.50 bits
contrast_name = {'cue_P', 'cue_V', 'cue_C', 'cue_G',...
    'cueXcue_P', 'cueXcue_V', 'cueXcue_C', 'cueXcue_G',...
    'stim_P', 'stim_V', 'stim_C', 'stim_G',...
    'stimXcue_P', 'stimXcue_V', 'stimXcue_C', 'stimXcue_G',...
    'motor', ...
    'simple_cue_P', 'simple_cue_V', 'simple_cue_C',...
    'simple_cueXcue_P', 'simple_cueXcue_V', 'simple_cueXcue_C', ...
    'simple_stim_P', 'simple_stim_V', 'simple_stim_C',...
    'simple_stimXcue_P', 'simple_stimXcue_V', 'simple_stimXcue_C'};

Cognitive :: check data coverage

m = mean(con_data_obj);

m.dat = sum(~isnan(con_data_obj.dat) & con_data_obj.dat ~= 0, 2);

orthviews(m, 'trans') % display

SPM12: spm_check_registration (v7759) 06:52:21 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

Grouping contiguous voxels: 1 regions

ans = 1×1 cell array

{1×1 region}

Cognitive :: Plot diagnostics, before l2norm

drawnow; snapnow

[wh_outlier_uncorr, wh_outlier_corr] = plot(con_data_obj)

______________________________________________________________ Outlier analysis ______________________________________________________________ global mean | global mean to var | spatial MAD | Missing values | 0 images Retained 5 components for mahalanobis distance Expected 50% of points within 50% normal ellipsoid, found 18.03% Expected 3.05 outside 95% ellipsoid, found 4 Potential outliers based on mahalanobis distance: Bonferroni corrected: 4 images Cases 8 21 26 27 Uncorrected: 4 images Cases 8 21 26 27 Retained 17 components for mahalanobis distance Expected 50% of points within 50% normal ellipsoid, found 47.54% Expected 3.05 outside 95% ellipsoid, found 1 Potential outliers based on mahalanobis distance: Bonferroni corrected: 0 images Cases Uncorrected: 1 images Cases 48 Mahalanobis (cov and corr, q<0.05 corrected): 4 images Outlier_count Percentage _____________ __________ global_mean 2 3.2787 global_mean_to_variance 3 4.918 missing_values 0 0 rmssd_dvars 0 0 spatial_variability 1 1.6393 mahal_cov_uncor 4 6.5574 mahal_cov_corrected 4 6.5574 mahal_corr_uncor 1 1.6393 mahal_corr_corrected 0 0 Overall_uncorrected 5 8.1967 Overall_corrected 4 6.5574

SPM12: spm_check_registration (v7759) 06:52:50 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1 (all) /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1 /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

Grouping contiguous voxels: 1 regions

wh_outlier_uncorr = 61×1 logical array

wh_outlier_corr = 61×1 logical array

Cognitive :: run robfit

set(gcf,'Visible','on')
figure ('Visible', 'on');
drawnow, snapnow;

Cognitive :: remove outliers based on plot

con = con_data_obj;
disp(strcat("current length is ", num2str(size(con_data_obj.dat,2))))
current length is 61
%for s = 1:length(wh_outlier_corr)
   % disp(strcat("-------subject", num2str(s), "------"))
con.dat = con_data_obj.dat(:,~wh_outlier_corr);
con.image_names = con_data_obj.image_names(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×57 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [57×12 char]
              fullpath: [61×109 char]
           files_exist: [61×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0020.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
con.fullpath = con_data_obj.fullpath(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×57 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [57×12 char]
              fullpath: [57×109 char]
           files_exist: [61×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0020.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
con.files_exist = con_data_obj.files_exist(~wh_outlier_corr,:)
con = 
  fmri_data with properties:

          source_notes: 'Info about image source here'
                     X: []
                  mask: [1×1 fmri_mask_image]
          mask_descrip: 'REMOVED: CHANGED SPACE'
    images_per_session: []
                     Y: []
               Y_names: []
             Y_descrip: 'Behavioral or outcome data matrix.'
            covariates: []
       covariate_names: {''}
    covariates_descrip: 'Nuisance covariates associated with data'
       history_descrip: 'Cell array of names of methods applied to this data, in order'
       additional_info: [0×0 struct]
        metadata_table: [0×0 table]
                   dat: [99837×57 single]
           dat_descrip: []
               volInfo: [1×1 struct]
        removed_voxels: 0
        removed_images: 0
           image_names: [57×12 char]
              fullpath: [57×109 char]
           files_exist: [57×1 logical]
               history: {''  'Sampled to space of /Volumes/spacetop_projects_social/analysis/fmri/spm/univariate/model-02_CcEScA/1stLevel/sub-0003/con_0020.nii'  'Masked with REMOVED: CHANGED SPACE'  'Checked image files exist. All exist =   1'}
%end
disp(strcat("after removing ", num2str(sum(wh_outlier_corr)), " participants, size is now ",num2str(size(con.dat,2))))
after removing 4 participants, size is now 57

Cognitive :: plot diagnostics, after l2norm

imgs2 = con.rescale('l2norm_images');

Cognitive :: ttest

t = ttest(imgs2);

One-sample t-test Calculating t-statistics and p-values

orthviews(t)

SPM12: spm_check_registration (v7759) 06:53:03 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

ans = 1×1 cell array

{1×1 struct}

drawnow, snapnow;

fdr_t = threshold(t, .05, 'fdr');

Image 1 FDR q < 0.050 threshold is 0.021671 Image 1 46 contig. clusters, sizes 1 to 42845 Positive effect: 43207 voxels, min p-value: 0.00000000 Negative effect: 67 voxels, min p-value: 0.00196159

orthviews(fdr_t)

SPM12: spm_check_registration (v7759) 06:53:05 - 26/05/2022 ======================================================================== Display /Users/h/Documents/MATLAB/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1

ans = 1×1 cell array

{1×46 struct}

drawnow, snapnow;

create_figure('montage'); axis off

montage(fdr_t)

Setting up fmridisplay objects

sagittal montage: 573 voxels displayed, 42701 not displayed on these slices

sagittal montage: 816 voxels displayed, 42458 not displayed on these slices

sagittal montage: 517 voxels displayed, 42757 not displayed on these slices

axial montage: 8228 voxels displayed, 35046 not displayed on these slices

axial montage: 8943 voxels displayed, 34331 not displayed on these slices

ans =

drawnow, snapnow;